All cards found in the main set of the Pokémon Battle e Emerald collection are for use in conjunction with the Nintendoe-Reader. Each card scanned will populate one floor of Trainer Hill with the depicted Trainer. Two Trainers always inhabit one floor, thus in the event that an odd number of cards are scanned, the game will place a default Trainer for that floor as the final opponent. A maximum of eight cards may be scanned for a full Trainer Hill challenge, though any card scanned afterwards will replace the first.

The Pokémon each Trainer will use is dependent on the order the card is scanned; each opponent Pokémon's level will also be equal to the players' highest level Pokémon. The first card scanned for each floor also generates the layout depicted on that card's reverse. As with all battles conducted in Trainer Hill, no money or experience is awarded.